| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Iteratee.Bgzf
Description
Handling of BGZF files. Right now, we have an Enumeratee each for input and output. The input iteratee can optionally supply virtual file offsets, so that seeking is possible.
- data Block = Block {}
- decompressBgzfBlocks' :: MonadIO m => Int -> Enumeratee ByteString Block m a
- decompressBgzfBlocks :: MonadIO m => Enumeratee ByteString Block m a
- decompressBgzf :: MonadIO m => Enumeratee ByteString ByteString m a
- decompressPlain :: MonadIO m => Enumeratee ByteString Block m a
- maxBlockSize :: Int
- bgzfEofMarker :: ByteString
- liftBlock :: Monad m => Iteratee ByteString m a -> Iteratee Block m a
- getOffset :: Monad m => Iteratee Block m FileOffset
- data BgzfChunk
- isBgzf :: Monad m => Iteratee ByteString m Bool
- isGzip :: Monad m => Iteratee ByteString m Bool
- parMapChunksIO :: (MonadIO m, Nullable s) => Int -> (s -> IO t) -> Enumeratee s t m a
- compressBgzf :: MonadIO m => Enumeratee BgzfChunk ByteString m a
- compressBgzfLv :: MonadIO m => Int -> Enumeratee BgzfChunk ByteString m a
- compressBgzf' :: MonadIO m => CompressParams -> Enumeratee BgzfChunk ByteString m a
- data CompressParams = CompressParams {}
- compressChunk :: Int -> Ptr CChar -> CUInt -> IO ByteString
Documentation
One BGZF block: virtual offset and contents. Could also be a block of an uncompressed file, if we want to support indexing of uncompressed BAM or some silliness like that.
Constructors
| Block | |
Fields | |
decompressBgzfBlocks' :: MonadIO m => Int -> Enumeratee ByteString Block m a Source
Decompress a BGZF stream into a stream of Blocks, np fold parallel.
decompressBgzfBlocks :: MonadIO m => Enumeratee ByteString Block m a Source
decompressBgzf :: MonadIO m => Enumeratee ByteString ByteString m a Source
Decompress a BGZF stream into a stream of ByteStrings.
decompressPlain :: MonadIO m => Enumeratee ByteString Block m a Source
Decompresses a plain file. What's actually happening is that the
offset in the input stream is tracked and added to the ByteStrings
giving Blocks. This results in the same interface as decompressing
actual Bgzf.
Maximum block size for Bgzf: 64k with some room for headers and uncompressible stuff
bgzfEofMarker :: ByteString Source
The EOF marker for BGZF files. This is just an empty string compressed as BGZF. Appended to BAM files to indicate their end.
liftBlock :: Monad m => Iteratee ByteString m a -> Iteratee Block m a Source
Runs an Iteratee for ByteStrings when decompressing BGZF. Adds
internal bookkeeping.
getOffset :: Monad m => Iteratee Block m FileOffset Source
Get the current virtual offset. The virtual address in a BGZF stream contains the offset of the current block in the upper 48 bits and the current offset into that block in the lower 16 bits. This scheme is compatible with the way BAM files are indexed.
isBgzf :: Monad m => Iteratee ByteString m Bool Source
Tests whether a stream is in BGZF format. Does not consume any input.
isGzip :: Monad m => Iteratee ByteString m Bool Source
Tests whether a stream is in GZip format. Also returns True on a
Bgzf stream, which is technically a special case of GZip.
parMapChunksIO :: (MonadIO m, Nullable s) => Int -> (s -> IO t) -> Enumeratee s t m a Source
Parallel map of an IO action over the elements of a stream
This Enumeratee applies an IO action to every chunk of the input
stream. These IO actions are run asynchronously in a limited
parallel way. Don't forget to evaluate
compressBgzf :: MonadIO m => Enumeratee BgzfChunk ByteString m a Source
Like compressBgzf', with sensible defaults.
compressBgzfLv :: MonadIO m => Int -> Enumeratee BgzfChunk ByteString m a Source
compressBgzf' :: MonadIO m => CompressParams -> Enumeratee BgzfChunk ByteString m a Source
Compresses a stream of ByteStrings into a stream of BGZF blocks,
in parallel
data CompressParams Source
Constructors
| CompressParams | |
Fields
| |
Instances
compressChunk :: Int -> Ptr CChar -> CUInt -> IO ByteString Source